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benchsiDE Knowledgebase

benchsiDE is a bulk RNA-seq analysis application that runs entirely in a web browser. It computes normalization, differential expression, gene-set tests, module screens and cross-dataset comparisons locally, without sending data to a server. Each statistical routine is validated against its reference implementation.

This knowledgebase explains what each part of the application does, how it is computed, and how to interpret it. For task-oriented instructions, see the User Guide.

Start here

• Getting started
• Input formats
• Troubleshooting
• FAQ

Data preparation

• Identifiers and annotation
• Design types
• Filtering
• Normalization
• Quality control

Statistics

• Differential expression
• Covariates and paired designs
• Multiple contrasts
• Statistical power
• Gene-set testing
• Discovery screen
• Patterns and clustering
• Heatmaps
• Co-expression and hub genes

Comparing datasets

• Cross-dataset comparison
• Orthologs and homology families

Output and reproducibility

• Figures and exports
• Sessions, reports and methods text
• Validation and self-test

Background

• Privacy and architecture
• Limitations
• Glossary
• Citing benchsiDE and its data sources